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PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms

Artículo de investigación publicado en Frontiers in Microbiology

16 de marzo de 2018

ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants. From this exhaustive computational analysis we developed a new PCR-based technique, targeting a specific sequence in the conserved region, for the screening, capture and sequencing of these small plasmids, either specific for Enterobacteriaceae or specific for Pasteurellaceae. To validate this PCR-based system, we tested various collections of isolates from both bacterial families, finding that ColE1 replicons were not only highly prevalent in antibiotic-resistant isolates, but also present in susceptible bacteria. In Pasteurellaceae, ColE1 plasmids carried almost exclusively antibiotic resistance genes. In Enterobacteriaceae, these plasmids encoded a large range of traits, including not only antibiotic resistance determinants, but also a wide variety of genes, showing the huge genetic plasticity of these small replicons. Finally, we also used a metagenomic approach in order to validate this technique, performing this PCR system using total DNA extractions from fecal samples from poultry, turkeys, pigs and humans. Using Illumina sequencing of the PCR products we identified a great diversity of genes encoded by ColE1 replicons, including different antibiotic resistance determinants, supporting the previous results achieved with the collections of bacterial isolates. In addition, we detected cryptic ColE1 plasmids in both families with no known genes in their variable region, which we have named sentinel plasmids. In conclusion, in this work we present a useful genetic tool for the detection and analysis of ColE1 plasmids, and confirm their important role in the dissemination of antibiotic resistance, especially in the Pasteurellaceae family of bacteria




Ares M., Bernabe-Balas C., Santos-Lopez A., Baquero MR., Prasad KN., Cid D., Martin-Espada C., San Millan A. y Gonzalez-Zorn B..




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PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms

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PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms


Participantes:

Universidad ComplutenseServicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).

Universidad ComplutenseDepartamento de Sanidad Animal. Facultad de Veterinaria. Universidad Complutense (UCM).

Universidad Alfonso X El SabioDepartamento de Microbiología. Facultad de Veterinaria. Universidad Alfonso X El Sabio (UAX).

Department of Microbiology. Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS).

Comunidad de MadridInstituto Ramón y Cajal de Investigación Sanitaria (IRYCIS). Universidad Complutense (UCM). Universidad Autónoma de Madrid (UAM). Universidad de Alcalá (UAH). Salud Madrid. Comunidad de Madrid.

Comunidad de MadridServicio de Microbiología. Hospital Universitario Ramón y Cajal. Salud Madrid. Comunidad de Madrid.







Frontiers in Microbiology
FACTOR YEAR Q
4.259 2018

NLMID: 101548977

PMID: 29615998

ISSN: 1664-302X



TÍTULO: PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms


REVISTA: Front Microbiol


NUMERACIÓN: 9(469):1-15


AÑO: 2018


EDITORIAL: Frontiers Research Foundation


AUTORES: Ares M., Bernabe-Balas C., Santos-Lopez A., Baquero MR., Prasad KN., Cid D., Martin-Espada C., San Millan A. and Gonzalez-Zorn B..


PARTICIPANTES VISAVET


First
Manuel Ares Arroyo
Last
Bruno González Zorn

DOI: https://doi.org/10.3389/fmicb.2018.00469


CITA ESTA PUBLICACIÓN:

Ares M., Bernabe-Balas C., Santos-Lopez A., Baquero MR., Prasad KN., Cid D., Martin-Espada C., San Millan A. y Gonzalez-Zorn B. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms. Frontiers in Microbiology. 9(469):1-15. 2018. (A). ISSN: 1664-302X. DOI: 10.3389/fmicb.2018.00469


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